Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Reusable building blocks in biological systems.

  PMID 30958230 · PMC6303794 · Journal of the Royal Society, Interface · 2018 · 8 claims · 5 setups

  Has reproduction · 82

  Biological systems can be decomposed into phenotypic building blocks (PBBs) whose reusability ranges from single-use (condition-specific) to constitutive

  tissues mirna randomized est-based quantitative computational

• Distribution and effects of nonsense polymorphisms in human genes.

  PMID 18852891 · PMC2561068 · PloS one · 2008 · 8 claims · 8 setups

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  Nonsense SNPs occur at a lower density than nonsynonymous SNPs, indicating stronger purifying selection against premature stop codons than amino acid changes.

  genome genes nonsense snps genome-wide snp codon

• High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

  PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

  Full-text index only

  Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

  embryonic neural t-cells mm8 chip-seq chip-chip pwm

• The distribution of SNPs in human gene regulatory regions.

  PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

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  SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

  gene mammalian promoter experimentally genome-wide computational binding

• Periodicity of SNP distribution around transcription start sites.

  PMID 16579865 · PMC1448210 · BMC genomics · 2006 · 8 claims · 6 setups

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  SNP density around TSS shows a 146-nucleotide periodicity

  genome human-chimpanzee tss promoter snp sequence cpg

• Tumour-brain crosstalk restrains cancer immunity via a sensory-sympathetic axis.

  PMID 41639447 · PMC12935554 · Nature · 2026 · 8 claims · 8 setups

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  Lung adenocarcinoma (LUAD) induces increased innervation and functional/transcriptional engagement of vagal sensory neurons (VSNs)

  kras-g12d tumour-bearing vagal npy2r-ires-cre whole-mount aav neurite

• A comparative study on recombination activity in cattle.

  PMID 41942849 · PMC13067647 · Genetics, selection, evolution : GSE · 2026 · 8 claims · 8 setups

  Has reproduction · 93

  Genotype data with high systematic missingness across breeds and arrays can be streamlined and analysed with three complementary recombination-estimation approaches (HMM-based LINKPHASE3, deterministic hsphase, likelihood-based hsrecombi)

  six paternal alphasimr-simulated brown snp recombination simulation

• Analysis of concordance of different haplotype block partitioning algorithms.

  PMID 16356172 · PMC1343594 · BMC bioinformatics · 2005 · 7 claims · 7 setups

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  Each block partitioning algorithm infers blocks differing in number, size, and coverage under different SNP density and allele frequency conditions.

  simulated subsamples coalescent diversity-based ld-based

• Next-generation high-density self-assembling functional protein arrays.

  PMID 18469824 · PMC3070491 · Nature methods · 2008 · 8 claims · 7 setups

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  A next-generation NAPPA method produces high-density protein microarrays displaying over 1500 unique proteins with >90% expression success

  test high-density amine-coated array picogreen anti-gst fluorescently

• Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

  PMID 19909546 · PMC2779822 · BMC genomics · 2009 · 7 claims · 8 setups

  Full-text index only

  Density of mouse orthologs of human disease genes correlates with regions of conserved microsynteny in the mouse genome

  genes autosomes dog genome comparative blat sliding-window

• Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

  PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

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  ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

  paralogous human-mouse duplicated comparative ortholog binomial

• Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms.

  PMID 42028238 · PMC13100350 · Computational and structural biotechnology journal · 2026 · 8 claims · 5 setups

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  A Regulation Ratio (RR), calculated as the ratio of gene-length-normalized POP-seq peak density to ATAC-seq peak density, quantifies the relative balance of post-transcriptional versus transcriptional regulation for individual genes

  hek293 computational atac-seq pop-seq rna-seq

• Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

  PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

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  SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

  genome autosomal hapmap chromosome snp chromosomal minor

• Simple models of genomic variation in human SNP density.

  PMID 17553150 · PMC1919371 · BMC genomics · 2007 · 6 claims · 4 setups

  Full-text index only

  Hierarchical Poisson model B, which allows both the mutation-rate proxy (Beta-distributed Λ) and the ARG-size proxy (Gamma-distributed T) to vary, fits the observed SNP density distribution significantly better than models with only one or neither varying.

  genome observed simulated genome hierarchical coalescent

• Neuropixels Opto: combining high-resolution electrophysiology and optogenetics.

  PMID 42225964 · PMC13259958 · Nature methods · 2026 · 8 claims · 7 setups

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  Neuropixels Opto probes integrate 960 recording sites and two sets of 14 light emitters (blue and red) on a 70-μm-wide, 1-cm-long shank via monolithic CMOS+photonics integration

  neuropixels test visual hippocampus electrode optical light

• M(5)C-driven stabilization of SERPINB5 promotes cervical cancer progression and chemotherapy resistance.

  PMID 41673397 · PMC12921336 · Cell death & disease · 2026 · 8 claims · 8 setups

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  RNA m5C levels are globally and consistently elevated in cervical tumors compared to normal cervical tissue

  cervical hela nsun2 bisulfite bulk spatial

• Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.

  PMID 27756200 · PMC5069797 · BMC bioinformatics · 2016 · 8 claims · 5 setups

  Has reproduction · 75

  Roar, a method using PRE/POST read counts around annotated APA sites to compute an m/M ratio and a ratio-of-ratios (roar) statistic, detects differential 3'UTR shortening/lengthening from standard RNA-seq libraries.

  testes normal gene rna-seq sapas cdna

• Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

  PMID 16042802 · PMC1190169 · BMC genomics · 2005 · 7 claims · 6 setups

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  Achieving high-multiplexing/high-coverage multiplex PCR designs is subject to a computational phase transition as the SNP-pair compatibility probability crosses a critical threshold

  simulated real chromosome randomly simulation multiplex coverage-vs-n

• Population genomics of human gene expression.

  PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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  Gene expression levels in lymphoblastoid cell lines are a heritable trait

  ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl

• TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.

  PMID 41494038 · PMC12788660 · PLoS computational biology · 2026 · 8 claims · 6 setups

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  TEPEAK identifies and characterizes polymorphic TEs in populations without any prior TE sequence or loci information, using only a chromosome-level reference assembly.

  horse pooled sequences consensus whole-genome insertion hierarchical